Electrophoresis is a separation technique most often applied to the analysis of biological or other polymeric samples. It has frequent application to analysis of proteins and DNA fragment mixtures. The high resolution of electrophoresis has made it a key tool in the advancement of biotechnology. Variations of this methodology are used for DNA sequencing, isolating active biological factors associated with diseases such as cystic fibrosis, sickle-cell anemia, myelomas, and leukemia, and establishing immunological reactions between samples on the basis of individual compounds. Electrophoresis is an extremely effective analytical tool because it does not affect a molecule's structure, and it is highly sensitive to small differences in molecular charge and mass.
Electrophoresis in a polymeric gel, such as a polyacrylamide gel or an agarose gel, adds two advantages to an electrophoretic system. First, the polymeric gel stabilizes the electrophoretic system against convective disturbances. Second, the polymeric gel provides a porous passageway through which the molecules must travel. Since larger molecules will travel more slowly through the passageways than smaller molecules, use of a polymeric gel permits the separation of molecules by molecular size.
One common electrophoretic procedure is to establish solutions having different pH values at each end of an electric field, with a gradient range of pH in between. At a certain pH, the isoelectric point of a molecule is obtained and the molecule carries no net charge. As the molecule crosses the pH gradient, it reaches an isoelectric point and is thereafter immobile in the electric field. Therefore, this electrophoresis procedure separates molecules according to their different isoelectric points.
More specifically, this procedure is referred to as isoelectric focusing (IEF) wherein an electric field is applied to a molecule in a pH gradient to mobilize the molecule to a position in the pH gradient at which its net charge is zero, i.e., the isoelectric point of the molecule. It often is used to separate proteins in a mixture and as an aid in the characterization of biomolecules of unknown composition. Commercially available gradients maybe utilized in isoelectric focusing which consist of multicharged ampholytes, with closely spaced isoelectric values and high conductivity, which partition into a pH gradient upon application of an electric field. The ampholytes are generally provided in a support matrix, such as a polyacrylamide gel.
Because protein samples are actually ampholytes, when samples are loaded onto the gel and a current is applied, the compounds migrate through the gel until they come to their isoelectric point where they reach a steady state. Isoelectric focusing takes a long time (from about 3 to 30 hours) to complete because sample compounds move more and more slowly as they approach the pH in the gel that corresponds to their isoelectric points. Because the gradient ampholytes and the samples stop where they have no mobility, the resistivity of the system increases dramatically toward the end of the experiment, and the current decreases dramatically. For this reason, isoelectric focusing is usually run with constant voltage. Constant current application can lead to overheating of the system.
The combination of sodium dodecyl sulfate (SDS), CH3(CH2)10CH2OSO3Na, also known as lauryl sulfate, treatment of samples and polyacrylamide gel electrophoresis was first described in the late 1960s. SDS is an ionic surfactant which solubilizes and denatures proteins. The surfactant coats a protein through hydrophobic interactions with the polypeptide backbone, effectively separating most proteins into their polypeptide subunits. The majority of proteins to which SDS binds then unfold into linear molecules having a similar surface potential.
SDS-polyacrylamide gel electrophoresis (SDS-PAGE) allows separation of molecules strictly on the basis of size, i.e., molecular weight. When SDS-treated samples migrate into a gel and are electrophoresed, the principal difference is size or length. Smaller molecules travel through the matrix more quickly than those that are larger. The rate at which molecules migrate through a polyacrylamide gel is inversely linear with the logarithm of their molecular weight. Thus denatured samples can be analyzed alongside standards of known molecular weight to aid in the interpretation of a substance's physical size.
Two-dimensional (2D) electrophoresis is unique, offering an analytical method that is both reproducible and sensitive. It is referred to as 2D because it employs two different methods of electrophoresis, in two different dimensions, to produce one result. Each method separates the sample compounds based on different properties of each compound. The combination of the two methods gives better resolution of the compounds in the sample than could be achieved with either method alone. For example, each method alone may separate up to 100 components of a sample, whereas together they may separate up to 10,000 components.
A pair of electrophoretic techniques commonly employed in 2D analyses are the previously noted isoelectric focusing (IEF) and SDS-polyacrylamide gel electrophoresis (SDS-PAGE). IEF separates sample compounds according to isoelectric point, whereas SDS-PAGE separates the compounds by molecular weight. A 2D analytical technique using IEF and SDS-PAGE to separate total protein results in a gel having bands or spots in a random pattern. Each spot represents a unique component of a sample. A single charge difference in a component can be identified on the gel by a unique spot. This property of 2D electrophoresis, which allows identification of identical proteins that differ by one charge difference, has made it an invaluable technique for the molecular genetic community.
As noted, many proteins are separated by polyacrylamide gel electrophoresis (PAGE) (based on the molecular weight) or modified polyacrylamide gel isoelectric focusing (IEF) (based on molecular charge). Both of the techniques can be used in tandem in a two-dimensional approach for maximum resolution. Polyacrylamide gels are made by polymerizing the monomer, acrylamide, into long strands, and then linking the strands together with a ‘cross-linker’, usually N,N′-methylene-bis-acrylamide (bis). The relative proportions of these components will determine the separation characteristics of the gel. Isoelectric focusing is carried out in a PAGE gel that contains an immobilized pH gradient consisting of high molecular weight polyaminocarboxylic acid (ampholytes). The separation power of two dimensional polyacrylamide gel electrophoresis (2D PAGE) has often been exploited as part of isolation schemes for determining the amino acid sequence of unknown proteins from complex protein mixtures.
Particles can be manipulated by subjecting them to traveling electric fields. Such traveling fields are produced by applying appropriate voltages to microelectrode arrays of suitable design. Traveling electric fields are generated by applying voltages of suitable frequency and phases to the electrodes.
This technique of using traveling electric fields relates to an important method for separation and sorting of large particles and cells referred to as dielectrophoresis. Dielectrophoresis is defined as the movement of a polarisable particle in a non-uniform electric field. Essentially, the force arises from the interaction of the field non-uniformity with a field induced charge redistribution in the separated particle.
Particles are manipulated using non uniform electric fields generated by various configurations of electrodes and electrode arrays. As a general biotechnological tool, dielectrophoresis is extremely powerful. From a measurement of the rate of movement of a particle the dielectric properties of the particle can be determined. More significantly, particles can be manipulated and positioned at will without physical contact, leading to new methods for separation technology.
A powerful extension of dielectrophoresis separation is traveling wave dielectrophoresis (TWD) in which variable electric fields are generated in a system of electrodes by applying time varying electric potential to consecutive electrodes. Such a method of Traveling Wave Field Migration was described by Parton et al. in U.S. Pat. No. 5,653,859, herein incorporated by reference. Although satisfactory, this work is not directed to the field of protein analyses and in particular, to 2D gel electrophoresis techniques.
A microfluidic device for electrophoretic separation of biomolecules such as DNA and protein was described by Dunphy et al. in “Rapid Separation and Manipulation of DNA by a Ratcheting Electrophoresis Microchip (REM),” Proceedings of IMECE2002, Nov. 17–22, 2002 New Orleans, La., No. IMECE2002-33564, herein incorporated by reference. The device utilizes thousands of electrodes along the length of a microchannel. An electrical potential is applied across the electrodes and selectively varied to separate molecules within the microchannel into two groups using a ratcheting mechanism. This mechanism does not employ traveling waves. Although directed to the separation of biomolecules, this strategy is based upon micro device technology and is not readily compatible with conventional laboratory proteomic equipment. Moreover, the strategy described by Dunphy et al. is silent with regard to applications involving 2D gel electrophoretic techniques, and more significantly, to IEF. Accordingly, a need exists for a device and technique for utilizing electrostatic traveling waves in conjunction with 2D gel electrophoresis techniques and equipment.
Two-dimensional (2D) gel electrophoresis is the acknowledged workhorse for proteomic research because it is simple, has high capacity, and is able to identify all proteins resolved on the gel when coupled with a mass spectrometer. However, lengthy process time, difficulty in resolving low-abundance proteins, and poor reproducibility, among other factors, has limited its full potential to becoming the definitive tool for proteomics. The present invention addresses many of these issues with a new instrument design and technique to reduce processing time and increase resolution by reducing band broadening with electrostatic traveling waves (TW).